2015 06 03 - LOINC Workshop

2014 Regenstrief Institute and James Case

Using RELMA OrIn Search of the Missing LOINC

James T. Case MS, DVM, PhD, FHL7, FACMI Health Program Specialist, SNOMED CT National Library of Medicine Laboratory LOINC Meeting June 2015


The views and opinions expressed do not necessarily state or reect those of the U.S. Government, and they may not be used for adver?sing or product endorsement purposes.

Disclaimer


Acknowledgements LOINC Development Team

Clem McDonald, Dan Vreeman, Jami Deckard, David Baorto, Katy Holck, Swapna Abhyankar, Theresa Pritchard, Rachel Fuhr, Sara Armson

RELMA Development Team John Hook, Anandhi Sowmyan, James Dennis

LOINC CommiLee Supporters

NLM, Regenstrief InsJtute, Regenstrief FoundaJon, APTA, RSNA, the LOINC Premium Members and Donors


What will we cover today? Overview of LOINC Reviewing new RELMA features! Installing RELMA SeNng personal preferences Loading a Local ObservaJon File (LMOF) Searching for a LOINC Term Preparing LMOF for Mapping Review of Map Screen FuncJons SeNng Search Limits Mapping Local Terms to LOINC Viewing LOINC Term Details Proposing/SubmiNng New LOINC Terms ExporJng/PrinJng Mapped Terms Mapping your own LMOF data


Why are we doing this? Goals of Health Information Standards

Interoperability the ability to exchange informaJon between organizaJons

Comparability the ability to ascertain the equivalence of data from dierent sources

Data Quality the measurement of accessibility, completeness, accuracy and precision (and more)


Levels of Interoperability Basic allows data to be exchanged between computer systems Word processing documents, text messages

Func?onal describes the standard syntax (format) of the data Document templates, forms, data structures Message standards

Seman?c requires use of standardized content (vocabularies) within the data structure


Comparability Meaning of the data is consistent when shared among dierent parJes Erysipelas Human skin disease; Streptococcus Grp A Erysipelas Animal SepJcemia/dermaJJs; Erysipelothrix rhusiopathiae

Common terminology required Should work in the background

Words are not enough Codes uniquely idenJfy terms Vocabulary specialized, precise terms that remove ambiguity

Ontology describes nature of enJJes and their relaJons ClassicaJon groups related terms by category


Potential Uses of Health Data are Constrained by Data Quality Factors Data quality issues

Dierent for client/paJent communicaJons vs. clinical decision support vs. epidemiological analysis

O\en constrained by external forces e.g. criteria for diagnosis o\en diers from the criteria for reporJng

UnidirecJonal eect of data consolidaJon Detailed General General Detailed

This is a problem even when standard

terminologies are used


The Problem In a_empJng to arrive at the truth, I have applied everywhere for informaJon, but in scarcely an instance have I been able to obtain hospital records t for any purpose of comparison. If they could be obtained, they would enable us to decide many other quesJons They would show [subscribers] how their money was being spent [and] what amount of good was really being done with it

Florence Nightingale - Notes on a Hospital, 1873


Test comparisons

Lab A Test Name: Lyme Disease Serology Measures: B. burgdorferi Ab IgG Method: ELISA Scale: quan?ta?ve e.g.: Titer 1:40

Lab B Test Name: Lyme Disease An?body Measures: B. burgdorferi Ab IgM Method: Immune blot Scale: qualita?ve e.g.: Posi?ve

LOINC Code = 5062-5 LOINC Code = 6321-4

What you see in the order list


Why LOINC? Within one laboratory, local jargon terms

may be used which are usually well understood between colleagues, but

would not be suciently widely known for communicaJon with the outside world.

U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Proper3es and Units in the Clinical Laboratory Sciences Part VII. Proper3es and Units in Clinical Microbiology


LOINC 101 Emphasis on Laboratory

LOINC


5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

5193-8 LOINC Code

Hepa??s B virus surface Ab

ACnc

Pt

Ser

Qn

EIA

Component

Property Measured

Timing

System

Scale

Method

There are six major LOINC axes

Anatomy of a LOINC Term


NOT part of a LOINC Name Reason for the test (why it was ordered or the disease it

diagnoses)

TesJng instrument Specic details about the specimen Priority (e.g. STAT) Where tesJng was done Who did the test Test interpretaJon Pricing or cost Anything not part of naming the test Things from other elds in an HL7 arJfact


The substance or enJty that is measured, evaluated, or observed

Component/Analyte

- Sodium - Glucose - Brucella sp. organism - Inuenza A Virus anJgen - Cytomegalovirus Virus anJbody - Lipids.Total



Component Structure Analyte Name^Challenge^Adjustments

Formal analyte name Specify subanalytes May have subclasses

Challenge Two parts separated by post

Adjustments

Calcium Coronavirus Ag Calcium.ionized

1H post 100 g Glucose PO

post

Adjusted to pH 7.4


Mass: ObservaJons reported with mass (milligrams, grams, etc.) in the numerator of their units of measure

Substance: ObservaJons reported with moles or milliequivalents in the numerator of their units of measure

Cataly?c ac?vity: ObservaJons that report enzymaJc acJvity Arbitrary: Results that report arbitrary units in the numerator of their units

of measure (slowly being reJred) Threshold: Results that represent the relaJon between a value and some

established limit or cut-o Number: Counts

Property


The characterisJc or a_ribute of the analyte that is measured, evaluated, or observed

the most dicult LOINC axis

Major Categories


MCnc mass concentraJon (mass/unit vol; e.g. mg/dL) MCnt mass content (mass/unit mass; e.g. mg/Kg) NCnc number concentraJon (number/unit vol; e.g. num/mL) TmStp Jme CCnc catalyJc concentraJon (acJvity; e.g. kat/L) Prid presence or idenJty Imp impression/interpretaJon Find subjecJve or objecJve observaJon Type Kind-of

Property


the most dicult LOINC axis

Combine Major Categories with Subtypes for Full Property


Common Property Issues

Frac?on = Part/Whole NFr: % Eosinophils / leukocytes SFr: % HGB which is A2

Ra?o = mulJple analytes from same system

MCrto: BUN/CreaJnine in serum Rela?ve Ra?o = measures from dierent system

RelRto: Albumin.pericard d/Albumin.SerPl

Fraction versus Ratio


Important property changes ACNC was always a placeholder

For P/N results, changed to Threshold AddiJonal migraJons occurring gradually LOINC IDs being retained

Flavors of Threshold Property ThrSCnc Threshold Substance ConcentraJon ThrMCnc Threshold Mass ConcentraJon ThrACnc Threshold Arbitrary ConcentraJon

PR vs PRID Presence or absence of an analyte now represented as PR (presence)

For nominal results, property is sJll PRID


Pt - at a point in Jme 12H - a twelve hour collecJon 24H - a twenty four hour collecJon

Timing*

*non-Pt Jmings are usually associated with Rate Property

The interval of Jme over which the observaJon or measurement was made



System The system (context) or specimen type upon

which the observation was made.

Ser Ser/Plas Bld Ur Flu Tiss XXX

serum serum or plasma whole blood urine body fluid tissue specified elsewhere

photo via AlishaV



System Structure

Super System PaJent is the default Used to indicate

blood product unit bone marrow donor fetus

818-5:A Ag:ACnc:Pt:RBC^BPU:Ord: 54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom:

System^Super System

photo via Xurble


Scale Qn Ord Nom Nar

Quantitative continuous numeric can have operators ()

Ordinal Ranked set (1+, 2+, 3+)

Nominal unranked collection Taxonomy (e.g. bacteria)

Narrative

photo via puuikibeach



Scale (Special) OrdQn Ordinal or QuanJtaJve

Primarily used for anJmicrobial observaJons e.g. MIC reported as resistant, intermediate, suscepJble or as the mm diameter of the inhibiJon zone

Use is discouraged in other contexts MulJ structured text globs

e.g. chromatography output Use is discouraged

Doc Clinical documents Set Clinical a_achments (headers)


Method Only needed if interpretaJon aected

Dierent normal ranges Test sensiJvity/specicity

Generally listed at the generic level AggluJnaJon Enzyme Immunoassay Probe with target amplicaJon



Hierarchies LOINC Class

one per term arbitrarily assigned

One for each LOINC axis MulJ-axial

Component | System Separate download


Mapping Terms to LOINC Things to Remember

The thing ordered is not always the thing measured: Blood Culture live organism(s) idenJed VDRL Treponema pallidum Ab Urinalysis lots of dierent things

You must know the specics of the component being tested for (what actually being measured?)

The quesJon (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl) You are mapping the quesJon, not the answer!

Need to get the observaJon/result boundary correct. Sample values help substanJally


What is in LOINC? Content

Term structures Submi_ed units, Example UCUM units

aiming toward preferred units sorJng Synonyms Answer lists (increasing number) Text descripJons links to info sources about individual tests Panel structures Foreign language translaJons

And much more


RELMA Regenstrief LOINC Mapping Assistant


Download of latest version

The latest version of the installaJon le may be downloaded from:

h_ps://iu.box.com/relma69


Purpose of Tutorial Eliminate need to read the Users Manual Become familiar with RELMA features Provide some insight into mapping Jps/piyalls Help begin the mapping process for your insJtuJon

Hang with some really cool folks


LOINC les and indexes Manual and automated mapping funcJons RELMA tools transform local words in local le

User creates le of local term/name and codes

Assigns LOINC term to local test/ba_ery code Common tests subset to speed mapping Context sensiJve hierarchies for local use. Flexible Google-like search funcJons

RELMA Functions


New in This Version (Rel. 6.9) End of support for Windows XP.

Microso\ ends support or XP in April 2014. No longer tesJng RELMA on Windows XP. The December 2015 release (version 6.12) of RELMA will not run on Windows XP.

Proxy support. Congure it in the Windows Internet OpJons applet. (see RELMA manual for details)


New in This Version (Rel. 6.9) New search restricJons added (See "Advanced Search Syntax" secJon of the user guide ): "PanelType

Allows limitaJon of search results to a panel type categories. "LForms"

True/false restricJon - indicates if LOINC code can be viewed in LForms data widget tool.

"AssociatedObservaJons Contains one or more LOINC codes that point to an addiJonal list of terms associated with an observaJon.


New in This Version (Rel. 6.9) "Export full panel structure to Excel" opJon available on Search tab grid and the grid on the Mapping tab.

New column added to search grids - "LForms". A hyperlink that opens your default browser to the specied URL. Not all rows will have this eld populated.

"Panels, Forms & Surveys" screen has been completely restructured.

"Associated observaJon" terms displayed on comprehensive detail pages when available.


LOINC Web Site


Whats available to download? RELMA - mapping and browsing tool

HL7 message converter- Makes a database suitable for mapping

LOINC database and spreadsheets Accessory les (panels, forms, top 2000, etc.) LOINC User guide; RELMA User Guide Tools to assist language translaJons by part Tools for building databases to map from HL7 messages

Guidance documents for mappers


RELMA Highlights Browse-able hierarchies of LOINC parts Display search results in tree view Enhanced details view of terms/parts

References DescripJons Sample units

Empirically-derived common test list Empirically-derived common order list Special features for panels/forms Enhanced export/copy-paste opJons


Installing RELMA


Installation Steps Requires Windows (or VM on a Mac) Make sure you have enough free disk space!

2Gb is recommended

From CD - Start Run :\RELMA\Setup Specify installaJon directory

Life will be easier if you accept the default

Two database les installed RELMA.MDB LOINC Terms Database LMOF3.MDB Local Master ObservaJon File

Two sample les included Run from Start (All) Programs Regenstrief RELMA


File Locations Database and Ancillary Files

Windows Vista = C:\Users\Public\Documents\RELMA\ Windows 7, 8 = C:\Users\Public\Public Documents\RELMA\

Sample les Windows Vista = C:\Users\Public\Documents\RELMA\Samples\ Windows 7, 8 = C:\Users\Public\Public Documents\RELMA\Samples\


Running RELMA Version 6.9


Copyright Screen


Join the LOINC Community


LOINC crowdsourcing


Main Menu/Welcome Screen


Set Preferred Language

Click File, Set Preferred Language


Select Linguistic Variant(s)

Selecting a translation may require indexes to be built


LOINC Terms with Spanish Linguistic Variant

All Spanish!


Setting User Preferences


Select User Preferences From the File Menu

Set User Preferences

...or from Welcome Screen


Set User Preference Dialog

Startup Screen Preference

File Locations: (See prior slide for location)

Local Term Backup Tab


User Map Screen Preferences Click Map Screen Tab

Include/Exclude Battery Terms

Add comments on Mappings

Auto create search terms


User Detail Pages Preferences

Download detail pages from LOINC.org


Request Submission Preference

Preferred method of request submission


Local Backup Preferences


Importing Local Terms into RELMA


5 Ways to Load LMOF Files Direct entry into LMOF from within RELMA (painful)

Handy for individual entries/edits

Create an Access table that mimics the LMOF structure (less painful but tedious) Appendix A: RELMA Manual

Create a delimited ASCII le from your local test catalog (good choice)

Import Excel le Load directly from HL7 v2.x messages

Pulls data from OBR and OBX segments Stores NTE segment data


Constructing a Local Dataset Create extract of your test catalog with:

Ba_ery/Panel Code Ba_ery/Panel DescripJon or Name *Local Code *Test DescripJon or Name

Include Method if Important Units Example Values Laboratory SecJon


Creating Delimited ASCII File RELMA cant parse free text

Need to create separate elds Can use any of these delimiters

Tab, Semicolon, Comma, Space Can dene your own

Fields can be in any order Minimum required elds

Local Code Local DescripJon Units (highly recommended)


Entering New Local Terms into RELMA


Manual Enter/Edit

View/Add/Edit Local Terms


Edit Term Dialog

Edit\Add\Delete Terms Export Terms

Print Preview List Text alignment option

User assigned tags


Export Local Term File

Delimiters supported: Tab, comma, semicolon, bar (|)

Export to Microsoft Excel or Text File

Export assigned tags


Add Local Term

Click to Add to Current Working File

MICRO

BUBPLAGBUBONIC PLAGUE RRT PCR

Add tags


Search Local Term File

Enter Keyword from any Field

Calcium

Return to Full List

Tags panel only appears if tags have been assigned

Open or close tag list


Using tags to gilter local terms

Print preview local term gile

Congigure output prior to viewing and printing


Print Preview Local Term File

Only prints selected rows


Steps to Import Local Terms 1. Click Import Local Terms Bu_on from Main Menu

a) File>Import Local Terms from Delimited File 2. Locate your local terms text le 3. Name your Working Set (Mandatory)

a) LMOF database can contain mulJple work sets 4. Dene default secJon (OpJonal) 5. IdenJfy le delimiter 6. Assign elds to LMOF a_ributes

a) Ignore elds you dont need b) Combine elds if needed

7. Check Case-sensiJve if needed 8. Click Import.


Example Tab-Delimited File


Importing Local Files

Select Import Local Terms from Delimited File or Excel Spreadsheet


Navigate to File Location Select File and Click Open Sample giles stored in

RELMA Directory


Open File in RELMA

Name your working set. RELMA allows multiple sets in

LMOF database

Select your delimiter

Import Button


Fields Segregated

Assign LMOF Attribute

Assign working set name


Working set import LOINC Workshop OBR


Ready to Import

Minimum assignments

Now you can click the Import button!


Import tags

You can include tags in your import le that allow you to categorize your local terms

Fields in import funcJon allow assignment of Tag with


Local term gile with added tags

Tag terms


Assign tag values

Tag with gield assignment


Tagged local terms

Imported tags


Post-Processing of Local File

A\er import, RELMA Searches for terms (words) that it does not recognize

Stored in a le for future reconciliaJon


Importing Excel gile

Excel giles now appear along with text giles


Excel format for import


Local Term File Options


Change Local Term File

Select the Working Set

Current mapping status

Can delete local term set; not the active one


Alternative Pragmatic Way Use large set of HL7 messages AutomaJcally make dataset of:

OBR ID OBR descripJon OBX ID OBX descripJon Sample of results with

Real values Units Abnormal ags Normal ranges


Generate Local term gile from HL7 messages

Select Import Terms from HL7 File


Select File to Import

Select HL7 File


Specify HL7 File Name and Sample Size

Name the Local Term File (working set)

Select which codes to store

Skip import of sample values

Select the number of sample values


HL7 Messages Data Statistics


New Terms added to LMOF

New Battery Code

Click on Edit Term to see Sample Data


Sample Results for Observation New Test Code

Sample Values from Messages


Lenny LOINC says: Load the Sample Files Into RELMA now!

Import the two sample les provided Import_Sample_OBR.txt

Contains ba_ery code and descripJon

Sample_HL7.HL7 Contains test code and descripJon and sample values

Create 2 working sets Load your personal data set


Cleaning your data


Preparing your Data for Mapping

Improve mapping success by: Expanding abbreviaJons Standardizing colloquial terms Ignoring administraJve terms Standardizing Jme references

Can be done prior to imporJng Be_er to use tools built into RELMA


RELMA Cleaning Tools Use this tool to edit unknown terms

Only available if no language variant selected


Review Unknown Local Terms

May Re-Scan File for Unknown Terms


Replace Local Terms

Assign LMOF Attribute Replacement Options


RELMA Cleaning Tools Use this tool to make global substitutions


Term Substitution

Save this global substitution for only this working set


Lenny LOINC says: Begin to clean your

data now!

Using the OBR sample le or your own data, take 15-20 minutes to clean up these unrecognized terms


Searching for LOINC Terms


Comprehensive Search Only Tool


Search Window

Enter Search Terms

Limit to Specigic Units

Use different logic

Help File

Restrict Limits


Search Window

Common Tests selected Common Tests rank


RELMA Search Helpgile


Context Menu

Right click to bring up context menu


Changed search function Max words

Large number of results

Keyword ComponentWordCount restricts word count Restricting to Common

labs regines further


Search function - Answerlist

Large number of results

Restricting to terms that have answer lists


Answerlist details


New advanced search syntax Paneltype

Classies LOINC panel term in categories


New advanced search syntax LForms

This true/false eld indicates whether or not the LOINC term is available for viewing in the LForms data widget tool.

Restricting to terms that have answer lists


Lforms widget demo


New advanced search syntax AssociatedObservations

AddiJonal terms that are related to a order term.


Mapping Local Terms


Mapping Local Terms

Select your Working Set to Map File>Select Local Term File to Process

Select Map Local Terms to LOINC from Welcome Screen

Select the subset of terms to work with: All Mapped Unmapped

Set your Search Limits Set Search Limits Bu_on


Standard Mapping Window Features

Customizable grid View details of LOINC term New! Add searchable tags to local term Sort by column

Click column Custom Sort

Print or export results grid Spell check squiggly line to signify words not known to RELMA


Mapping Screen View or edit local term

Quick select button list

Custom Grid Congiguration

Enter local term number

User assigned tags


Congigure Grid

Reorder grid elements

Select elements to display

Reset Default Congiguration Visually resize elements


Quick choice buttons

Viewing LOINC term detail


View Local Term Details

Select level of detail to display

Can scroll through returned subset of

terms

Change text size

Can scroll down a single formatted page


Details Text Size Select text size


Select detail display level

Select level of detail to display


Standard Mapping Screen

Begin a search (or hit enter) EEK! Whatll I

do?!



Click to show words

used in search


Initial Mapping Results

Use term checkbox

Number of LOINC terms containing

keyword Battery terms included in search


Revised Mapping Results

Number of matching

records found


Re-revised Mapping Results

Number of matching

records found Match units selected



Clear all input gields

Enter keywords here

CANINE DISTEMPER VIRUS IF



Navigate through the local terms


Tabbed Access to Functions

Navigate to Functions from Mapping Page

Switch between Grid and Tree Views


Tree View


Tree View Results displayed hierarchically

Dened by the mulJ-axial hierarchy in search restricJons (covered later)

Map to a term in tree by clicking Map bu_on or double clicking term Only to rows that have LOINC Codes


Tree View

Cannot map to terms

representing LOINC parts

Can map to terms with LOINC Codes

Tree Navigation Buttons


Assigning a LOINC Map

Highlight correct term

Click Map Button (or doubleclick)


Adding Mapping Comments

If comments option is selected, prompt appears

Check with Frank in Chemistry


Assigning a LOINC Map

LOINC Term Assigned


View Panel Children

Select View Panel Children from context menu


Panel Children


Congigure Export Options

Output Options Include

column headers Save Congiguration and/or Export


Excel Export Format


Linked answer lists

Adds answer list IDs to the answer tab of a panel export

Allows linkage using the AnswerlistID with the LOINC codes and the answer to see which answers go with a specic LOINC


Search for a panel

Search for panel or LOINC code

Find the panels associated


Get panel details and export

Export the full panel structure


Detailed answer data

Answer tab

LOINC code AnswerListID Answer String


More on Searching Search Screen


Basic Search Syntax Special Character(s)

Example Deni?on

Inuenza virus A Linked terms must appear together

AND Morphine AND Opiates

Both terms must appear in the search result term

OR Inuenza OR Parainuenza

Either or both terms must appear in the search result term

NOT Inuenza NOT equine Excludes terms with the word following the NOT. Cannot be used alone.

? Gluc?se (glucose,glucase)

SubsJtutes a single character in the string. Cannot be used as the rst character; cannot be used in phrases

* Gluc*se (glucose, glucuronidase, etc.)

SubsJtute mulJple characters in the string. Cannot be used as the rst character; cannot be used in phrases


Search Qualigiers

Includes Glucuronidase, Glucosidase,

Glucosylceramidase, etc.

Detailed help available


Combining Search Terms

Reduced number of terms

Exclude Glucosidase


Advanced Search Syntax based on Google-like search syntax

Parameter Descrip?on

+ Term must be included in search

- Term must be excluded from the search

( ) Group terms for subquery (i.e. A OR B; A AND B)

Fieldname: Limit term search to the associated eld (e.g. Component: glucose)

Fieldname:() Group mulJple terms in a single eld

~ Fuzzy search (e.g. Hemoilus~)

~ Proximity search for mulJple terms (e.g. funcJon panel~1)

{}, [] Upper and lower bounds; {} exclusive, [] inclusive

\ Special character escape


Applying advanced search

91 terms



33 terms



19 terms



8 terms


Limiting Searches


Setting Search Limits

Narrows search to specic subset of LOINC terms Reduces number of candidate terms Limits can be applied to all components Component a_ribute can be further restricted by number of words

Tree structure allows for hierarchical constraints


General Search Constraints Controls features including:

Limit to LOINC terms compaJble with submi_ed units Forced match with any specimen contained in name Method-less terms only Restrict by class type Remove lateralized terms

Use carefully or search may not be successful (Note parallel control switches at bo_om of screen)



Click Hierarchy & Search Limits Tab


Setting search limits Can also set most of them by toggling bu_ons

at the bo_om of the screen

Toggle Buttons


Search Constraints

Expanded predegined, general search constraints

Attribute trees

Limit to LOINC terms consistent with local units


Terms Consistent with Units

Only terms consistent with mmol/L appear



Specimen constraints


Terms Consistent with Specimen

CSF

Enter default Specimen


Terms Consistent with Specimen

Only CSF Terms are returned



Exclude laterality


Exclude laterality

Laterality terms



Restrict to common orders


Restriction to common orders

Large number of candidates Common orders

rank



Methodless Terms Restriction

Override Methodless Terms Restriction


Limit to Methodless Terms

Both method and method-less terms


Limit to Methodless Terms

Only Methodless Terms Appear


More on Methodless Terms Some LOINC categories do not have methodless terms

Checking methodless only will remove these from view on results grid

Checking addiJonal box allows these to be seen


Methodless Only Unchecked

All terms returned


Methodless Only Checked

Only Methodless terms returned

Differ in one or more components


Conditional Methodless

More terms returned

No method-less term; all shown



Include Trial, Deprecated or Discouraged LOINC Codes with

Returned Terms


Include Deprecated LOINC Terms

Deprecated LOINC Terms appear as Strikethrough Text with a Do Not

Symbol

You cannot map to deprecated LOINC terms

The map button is grayed out if one of these terms is selected

Discouraged LOINC Terms appear as an inverted triangle


Favor Property Restriction

Favor one type of property over others

All other components being equal MCnc

only will be displayed


Order/Observation Restriction

Order or Observation preference


LOINC Hierarchies Class Tree

Three top-level branches

Tree Navigation Buttons


Before Class Restriction

Large number of candidate terms

Many terms have class of CHAL


Search Trees

Restrict eligible tests to non-challenge

chemistry tests only


Following Class Restriction

Only Non-Challenge Chemistry tests

returned


System Hierarchy


Component Hierarchy

Show the LOINC Codes associated with these

components

Click on details for more information about the

selection


Details Screen LOINC Part


Show Associated LOINCs


LOINC Term Details Screen


Tree Export Tools

Congigure Export Format

Export according to Congiguration


Tree Export Congiguration


RELMA - Tree Features All trees operate the same way Shows terms spelled out Can expand and collapse parts or all of tree. Tree is string searchable Search can be based on one or more branches of a tree with or without other criteria

Use Clear Most Limits bu_on on Mapping Screen to remove all tree selecJons


LOINC Part Search Same look as term search Uses same Google-like query language

Extremely fast Include and exclude criteria ParJal string matching (using wildcards)

LOINC CLASS values may now be search using "ClassList:" eld

Demo Campylobacter fetus, not Ab


LOINC Answer List Search

Nominal LOINC terms are now required to be submi_ed with answer lists.

Finding answer lists and the use of them can be done with Answer List Search tab


Answer List Search

Answer Lists associated with LOINC term New! Revised and expanded answer list export options


Navigating through the Mapping Process


Limit eort to one lab secJon at a Jme and focus experJse

Chemistry and hematology will be easiest For manufactured assays, use package insert as source informaJon

Sample results give clue to property and scale Consider prioriJzing by frequency of use

LOINC Mapping Tactics


Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.


More LOINC Mapping Tactics Try using method-less terms rst

Specic methods can be transmi_ed in: OBX17 (v2.x), ObservaJon.methodCode (v3.0)

Examine local units or real results to verify correct property and scale ProperJes are rarely disJnguishable in test names

You dont have to do it all at one siNng Use the Unmapped funcJon to return where you le\ o

With every release - Update previous mappings to idenJfy deprecated terms


Common Mapping Issues

Locally Dened Test Name Ambiguity Reuse of local test code

Analyte-free Local Test Names (Miscellaneous serology, PCR)

Incongruent Value sets (Scale ambiguity) Result vs. InterpretaJon Available LOINC Terms too Specic/General Panel vs. Discrete Test

Common in Microbiology


Using your Mapped Terms

Print results of LOINC Mapping Export to File


Congigure Export Format

Context Sensitive Export Congiguration


LMOF Export Congiguration

Select Fields to Export

Select Export Format

Save Congiguration and Export


Print Mapped Terms from View/Add/Edit Menu

May highlight terms to be printed

Click Print button to Preview output


Formatted Report Output

Click Print button to output formatted report


Excel Export


Lab Auto Mapper

Run in batch mode to nd N- closest terms Can then use this output to do nal mapping Again units are VERY important Can pick all limits available to regular mapping


Picking the Lab Auto Mapper


Lab Auto Mapper Start Screen

Maximum number of terms to return

Can restrict search to common tests


Lab Auto Mapper Start Screen

Terms used for mapping

Local test code


Lab Auto Mapper - Mapping Screen


Exporting Mapped Terms

Export Terms to Delimited File


Export Terms Dialog

Check Fields you wish to export

Select Delimiter

Select Term Set

Direct export to Excel

Select gile location


Other RELMA Features


Panels, Forms and Survey Review

Review Panels, Forms and Surveys

Review Panels, Forms and Surveys


Panels, forms and surveys revised display

Expand category to see panels

Double-click panel test to see components


Expanded Panel Detail


Expanded Clinical Panel


Clinical Panels

Find where a term has been used

35089-2, 35090-0


LOINC Term Panel Usage


HIPAA Attachments

View Various HIPAA Attachments


HIPPA Attachment Tree


Expanded Attachment Data


Cant gind the term you want?


Search Hints and Tips Keywords with zero frequency are ignored

May need to rephrase use synonym Some causes for no returned terms

Too many keywords in search uncheck some Limits applied that dont make sense

E.g. Method-less tests plus Method tree set to EIA Did not nd and revise words not in RELMA

Local units not in RELMA

Units are GREAT discriminators You may have tests that need to be added to LOINC


Proposing New LOINC Terms


Proposing New Terms Make sure the term is really needed

Think of other names for the same concept Avoid detailed methods or localizaJons Is the disJncJon really important?

Supply sucient annotaJon to jusJfy the new term Package inserts, sample reports (email to Regenstrief) The more the be_er!

Construct new terms within RELMA File>Propose a new LOINC

Linked to the trees to allow browsing Can review and submit them to LOINC from within RELMA


Propose new LOINC terms

Select Propose a new LOINC


Required gields in red

Navigate through proposed terms

Create new term, save current term

or Exit form


Preview Proposed Terms

Review your new terms


Review Proposed Terms

All proposed terms fully editable

Choose whether to send or postpone

X

X X

James T. Case DVM, PhD

NIH/NLM

[email protected]

301-555-1314

301-555-1315

Direct submission via web


Submit Proposed Terms

Add additional information, if

necessary Add attachments


Submitting New Terms Must supply name, organizaJon, phone and email of submi_er

Must select at least one proposed term to send

Congure export does not aect submission output

Email resulJng le to Regenstrief


Use Existing Terms as Template

Select your closest match

Click the Propose Term button


Use Existing Terms as Template

All required components gilled in


Using LOINC and SNOMED Together


Where do LOINC and SNOMED Fit?

LOINC represents the quesJon: Is there any Botulism toxin in my specimen? (33708-9)

Organisms idenJed in specimen? (634-6)

SNOMED represents the answer: NegaJve (SCTID 260385009) E. coli O157:H7 (SCTID 103429008)

Remember:


Where do LOINC and SNOMED Fit? In an HL7 message, LOINC may be used:

In OBR-4 (Universal Service IdenJer) In OBX-3 (ObservaJon IdenJer

SNOMED may be used: In OBX-5 (where nominal values are needed) Almost anyplace else in an HL7 message where coded values are needed


The code is from SNOMED

The code is from LOINC

OBX-5: Data A code for L.

monocytogenes

A code that identigies the data type in OBX-5 as a

coded element

OBX: With a Coded Value

OBX-3:A code that identigies the data in

OBX-5 (Listeria culture)

OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT


HL7 2.5 Example (ER-7 format) MSH|^~\&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|

LABGL1199510221838581| P| 2.3||| NE| NE PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^ Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090 OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^

UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium

^SCT|||||| F||| 199812292128|| CA20837 OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility

Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN

OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate

^SCT|||||| F||| 199812300934|| CA20837 OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934||

CA20837 OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F|||

199812300934|| CA20837

First Order OBR (Culture and ID)

First Result (Culture and ID) First Result

(Culture and ID) Second Result(s)

OBXs

First Result Value (SNOMED)

First Result Description OBX (LOINC)

Second Order OBR (Susceptibility)


Q and A Session


Exercise Map your own data

2015 06 03 - LOINC Workshop

Documents

Transcript of 2015 06 03 - LOINC Workshop